Starting phenix.real_space_refine on Sat Jul 20 11:22:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x24_32957/07_2024/7x24_32957_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x24_32957/07_2024/7x24_32957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x24_32957/07_2024/7x24_32957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x24_32957/07_2024/7x24_32957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x24_32957/07_2024/7x24_32957_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x24_32957/07_2024/7x24_32957_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians K 3 8.98 5 Al 1 5.89 5 P 5 5.49 5 Mg 1 5.21 5 S 50 5.16 5 C 6673 2.51 5 N 1651 2.21 5 O 1898 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 83": "OE1" <-> "OE2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A ASP 275": "OD1" <-> "OD2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 688": "OE1" <-> "OE2" Residue "A PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 765": "OD1" <-> "OD2" Residue "A ASP 782": "OD1" <-> "OD2" Residue "A TYR 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 983": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1031": "OD1" <-> "OD2" Residue "B ASP 114": "OD1" <-> "OD2" Residue "B ASP 125": "OD1" <-> "OD2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10286 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7666 Classifications: {'peptide': 986} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 36, 'TRANS': 949} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2255 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 257} Chain: "A" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 323 Unusual residues: {' K': 3, ' MG': 1, 'ALF': 1, 'CLR': 2, 'PCW': 5} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.72, per 1000 atoms: 0.65 Number of scatterers: 10286 At special positions: 0 Unit cell: (122.01, 103.75, 171.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) K 3 19.00 S 50 16.00 P 5 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1898 8.00 N 1651 7.00 C 6673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 277 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied NAG-ASN " NAG B 401 " - " ASN B 158 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.06 Conformation dependent library (CDL) restraints added in 2.0 seconds 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2350 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 11 sheets defined 49.7% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 60 through 69 Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 108 through 111 removed outlier: 3.532A pdb=" N GLY A 111 " --> pdb=" O GLN A 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 108 through 111' Processing helix chain 'A' and resid 113 through 134 Processing helix chain 'A' and resid 141 through 163 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.685A pdb=" N PHE A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 169 through 174' Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.652A pdb=" N THR A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 276 Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 294 through 324 Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 347 through 365 removed outlier: 3.543A pdb=" N THR A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 4.187A pdb=" N THR A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 379' Processing helix chain 'A' and resid 429 through 440 Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'A' and resid 462 through 477 Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 522 through 529 Processing helix chain 'A' and resid 543 through 560 Processing helix chain 'A' and resid 610 through 621 Processing helix chain 'A' and resid 632 through 644 Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'A' and resid 678 through 684 removed outlier: 3.730A pdb=" N ASP A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'A' and resid 730 through 732 No H-bonds generated for 'chain 'A' and resid 730 through 732' Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 751 through 758 Processing helix chain 'A' and resid 768 through 793 removed outlier: 3.857A pdb=" N THR A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 809 removed outlier: 3.673A pdb=" N GLU A 798 " --> pdb=" O SER A 794 " (cutoff:3.500A) Proline residue: A 801 - end of helix Processing helix chain 'A' and resid 815 through 825 Processing helix chain 'A' and resid 827 through 834 Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 842 through 846 removed outlier: 3.504A pdb=" N ARG A 846 " --> pdb=" O ILE A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 867 Processing helix chain 'A' and resid 870 through 887 Processing helix chain 'A' and resid 891 through 896 removed outlier: 3.785A pdb=" N ILE A 896 " --> pdb=" O THR A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 903 Processing helix chain 'A' and resid 919 through 950 Processing helix chain 'A' and resid 955 through 960 Processing helix chain 'A' and resid 964 through 984 removed outlier: 3.915A pdb=" N TRP A 968 " --> pdb=" O ASN A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1002 Processing helix chain 'A' and resid 1004 through 1025 Processing helix chain 'A' and resid 1030 through 1035 Processing helix chain 'B' and resid 29 through 59 Processing helix chain 'B' and resid 94 through 110 removed outlier: 4.120A pdb=" N TYR B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N TYR B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 118 removed outlier: 6.162A pdb=" N ASP B 114 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N SER B 115 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.985A pdb=" N TYR B 167 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY B 168 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 218 through 226 removed outlier: 3.591A pdb=" N LYS B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP B 223 " --> pdb=" O ASP B 219 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 removed outlier: 3.617A pdb=" N PHE B 236 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 185 Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 205 removed outlier: 6.662A pdb=" N CYS A 261 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL A 225 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLU A 263 " --> pdb=" O CYS A 223 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N CYS A 223 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE A 269 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU A 217 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE A 271 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE A 215 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 205 removed outlier: 6.662A pdb=" N CYS A 261 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL A 225 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLU A 263 " --> pdb=" O CYS A 223 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N CYS A 223 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE A 269 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU A 217 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE A 271 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE A 215 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 370 removed outlier: 6.225A pdb=" N GLY A 743 " --> pdb=" O MET A 760 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU A 762 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA A 745 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL A 724 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ILE A 744 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL A 726 " --> pdb=" O ILE A 744 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N MET A 746 " --> pdb=" O VAL A 726 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N GLY A 728 " --> pdb=" O MET A 746 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 384 " --> pdb=" O ALA A 725 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N THR A 727 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N CYS A 386 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ILE A 385 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL A 628 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N SER A 387 " --> pdb=" O VAL A 628 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL A 625 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N PHE A 702 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N MET A 627 " --> pdb=" O PHE A 702 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 408 through 411 removed outlier: 3.658A pdb=" N HIS A 402 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N PHE A 595 " --> pdb=" O TYR A 571 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N TYR A 571 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N PHE A 597 " --> pdb=" O HIS A 569 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS A 569 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY A 599 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 515 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS A 487 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 408 through 411 removed outlier: 3.658A pdb=" N HIS A 402 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N CYS A 530 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE A 597 " --> pdb=" O CYS A 530 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N THR A 532 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N GLY A 599 " --> pdb=" O THR A 532 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N MET A 534 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 12.531A pdb=" N LEU A 601 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 444 through 445 Processing sheet with id=AA8, first strand: chain 'A' and resid 910 through 911 Processing sheet with id=AA9, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AB1, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.175A pdb=" N ILE B 88 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 123 through 124 485 hydrogen bonds defined for protein. 1377 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3192 1.34 - 1.46: 1544 1.46 - 1.58: 5660 1.58 - 1.69: 10 1.69 - 1.81: 83 Bond restraints: 10489 Sorted by residual: bond pdb=" C11 PCW A1104 " pdb=" O3 PCW A1104 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C11 PCW A1106 " pdb=" O3 PCW A1106 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C11 PCW A1109 " pdb=" O3 PCW A1109 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C11 PCW A1108 " pdb=" O3 PCW A1108 " ideal model delta sigma weight residual 1.326 1.452 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C31 PCW A1104 " pdb=" O2 PCW A1104 " ideal model delta sigma weight residual 1.333 1.458 -0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 10484 not shown) Histogram of bond angle deviations from ideal: 89.72 - 107.70: 388 107.70 - 125.68: 13663 125.68 - 143.65: 138 143.65 - 161.63: 0 161.63 - 179.61: 2 Bond angle restraints: 14191 Sorted by residual: angle pdb=" F1 ALF A1111 " pdb="AL ALF A1111 " pdb=" F2 ALF A1111 " ideal model delta sigma weight residual 108.68 179.31 -70.63 3.00e+00 1.11e-01 5.54e+02 angle pdb=" F3 ALF A1111 " pdb="AL ALF A1111 " pdb=" F4 ALF A1111 " ideal model delta sigma weight residual 109.63 179.61 -69.98 3.00e+00 1.11e-01 5.44e+02 angle pdb=" F2 ALF A1111 " pdb="AL ALF A1111 " pdb=" F4 ALF A1111 " ideal model delta sigma weight residual 110.21 89.78 20.43 3.00e+00 1.11e-01 4.64e+01 angle pdb=" F1 ALF A1111 " pdb="AL ALF A1111 " pdb=" F3 ALF A1111 " ideal model delta sigma weight residual 109.69 89.72 19.97 3.00e+00 1.11e-01 4.43e+01 angle pdb=" F2 ALF A1111 " pdb="AL ALF A1111 " pdb=" F3 ALF A1111 " ideal model delta sigma weight residual 109.59 90.14 19.45 3.00e+00 1.11e-01 4.20e+01 ... (remaining 14186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.79: 6325 32.79 - 65.57: 183 65.57 - 98.36: 17 98.36 - 131.15: 3 131.15 - 163.93: 4 Dihedral angle restraints: 6532 sinusoidal: 2874 harmonic: 3658 Sorted by residual: dihedral pdb=" CB CYS B 159 " pdb=" SG CYS B 159 " pdb=" SG CYS B 175 " pdb=" CB CYS B 175 " ideal model delta sinusoidal sigma weight residual -86.00 -137.28 51.28 1 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" N PCW A1106 " pdb=" C4 PCW A1106 " pdb=" C5 PCW A1106 " pdb=" O4P PCW A1106 " ideal model delta sinusoidal sigma weight residual -66.66 97.27 -163.93 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" N PCW A1108 " pdb=" C4 PCW A1108 " pdb=" C5 PCW A1108 " pdb=" O4P PCW A1108 " ideal model delta sinusoidal sigma weight residual 293.34 143.48 149.86 1 3.00e+01 1.11e-03 1.99e+01 ... (remaining 6529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1405 0.067 - 0.134: 187 0.134 - 0.201: 9 0.201 - 0.269: 3 0.269 - 0.336: 2 Chirality restraints: 1606 Sorted by residual: chirality pdb=" C2 PCW A1104 " pdb=" C1 PCW A1104 " pdb=" C3 PCW A1104 " pdb=" O2 PCW A1104 " both_signs ideal model delta sigma weight residual False -2.32 -2.66 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C13 CLR A1107 " pdb=" C12 CLR A1107 " pdb=" C14 CLR A1107 " pdb=" C17 CLR A1107 " both_signs ideal model delta sigma weight residual False -2.93 -2.66 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C13 CLR B 402 " pdb=" C12 CLR B 402 " pdb=" C14 CLR B 402 " pdb=" C17 CLR B 402 " both_signs ideal model delta sigma weight residual False -2.93 -2.70 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1603 not shown) Planarity restraints: 1770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 401 " -0.301 2.00e-02 2.50e+03 2.53e-01 8.01e+02 pdb=" C7 NAG B 401 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B 401 " -0.189 2.00e-02 2.50e+03 pdb=" N2 NAG B 401 " 0.433 2.00e-02 2.50e+03 pdb=" O7 NAG B 401 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 686 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A 687 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 687 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 687 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 128 " 0.007 2.00e-02 2.50e+03 1.13e-02 2.23e+00 pdb=" CG PHE A 128 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 128 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 128 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 128 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 128 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 128 " 0.000 2.00e-02 2.50e+03 ... (remaining 1767 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.69: 185 2.69 - 3.30: 11618 3.30 - 3.92: 19682 3.92 - 4.53: 27006 4.53 - 5.14: 42531 Nonbonded interactions: 101022 Sorted by model distance: nonbonded pdb=" F1 ALF A1111 " pdb="MG MG A1112 " model vdw 2.080 2.120 nonbonded pdb=" OD2 ASP A 388 " pdb="MG MG A1112 " model vdw 2.090 2.170 nonbonded pdb=" O THR A 390 " pdb="MG MG A1112 " model vdw 2.105 2.170 nonbonded pdb=" O ILE A 907 " pdb=" NH2 ARG A 923 " model vdw 2.252 2.520 nonbonded pdb=" OD2 ASP A 388 " pdb=" F1 ALF A1111 " model vdw 2.272 2.390 ... (remaining 101017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.990 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 10489 Z= 0.393 Angle : 1.212 70.627 14191 Z= 0.466 Chirality : 0.047 0.336 1606 Planarity : 0.007 0.253 1769 Dihedral : 15.936 163.933 4173 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.24), residues: 1259 helix: 1.45 (0.23), residues: 525 sheet: -0.33 (0.39), residues: 164 loop : -0.67 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 968 HIS 0.003 0.001 HIS A 868 PHE 0.025 0.002 PHE A 128 TYR 0.015 0.001 TYR A 805 ARG 0.007 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 LYS cc_start: 0.7743 (tttp) cc_final: 0.7481 (mtpp) REVERT: A 421 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6735 (mm-40) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2572 time to fit residues: 54.0150 Evaluate side-chains 125 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 343 ASN ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 10489 Z= 0.326 Angle : 0.639 8.195 14191 Z= 0.324 Chirality : 0.047 0.168 1606 Planarity : 0.005 0.050 1769 Dihedral : 12.981 148.447 1790 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.73 % Allowed : 9.18 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1259 helix: 1.14 (0.23), residues: 535 sheet: -0.45 (0.40), residues: 158 loop : -0.74 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1001 HIS 0.004 0.001 HIS A 868 PHE 0.013 0.002 PHE B 38 TYR 0.021 0.002 TYR A 881 ARG 0.004 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.184 Fit side-chains REVERT: A 87 ARG cc_start: 0.6142 (ttt-90) cc_final: 0.5545 (ptm160) REVERT: A 365 LYS cc_start: 0.7783 (tttp) cc_final: 0.7462 (mtpp) REVERT: A 421 GLN cc_start: 0.7388 (mm-40) cc_final: 0.6956 (mm110) outliers start: 8 outliers final: 6 residues processed: 141 average time/residue: 0.2687 time to fit residues: 51.8003 Evaluate side-chains 134 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 219 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 245 HIS ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10489 Z= 0.158 Angle : 0.516 7.453 14191 Z= 0.266 Chirality : 0.042 0.155 1606 Planarity : 0.004 0.047 1769 Dihedral : 12.291 150.183 1790 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.01 % Allowed : 11.39 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.24), residues: 1259 helix: 1.53 (0.23), residues: 530 sheet: 0.01 (0.41), residues: 147 loop : -0.71 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1001 HIS 0.002 0.001 HIS A 569 PHE 0.011 0.001 PHE A 935 TYR 0.016 0.001 TYR A 881 ARG 0.003 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6728 (mt) REVERT: A 87 ARG cc_start: 0.6148 (ttt-90) cc_final: 0.5636 (ptm160) REVERT: A 365 LYS cc_start: 0.7788 (tttp) cc_final: 0.7485 (mtpp) REVERT: A 421 GLN cc_start: 0.7275 (mm-40) cc_final: 0.6733 (mm110) REVERT: A 472 SER cc_start: 0.8291 (m) cc_final: 0.7907 (p) REVERT: A 473 GLU cc_start: 0.7553 (tp30) cc_final: 0.7235 (tp30) outliers start: 11 outliers final: 6 residues processed: 138 average time/residue: 0.2617 time to fit residues: 49.3499 Evaluate side-chains 131 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10489 Z= 0.241 Angle : 0.561 7.769 14191 Z= 0.287 Chirality : 0.044 0.189 1606 Planarity : 0.004 0.050 1769 Dihedral : 12.471 152.598 1790 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.47 % Allowed : 13.22 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.24), residues: 1259 helix: 1.42 (0.23), residues: 530 sheet: -0.14 (0.40), residues: 149 loop : -0.71 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1001 HIS 0.003 0.001 HIS A 868 PHE 0.013 0.002 PHE A 935 TYR 0.022 0.001 TYR A 805 ARG 0.002 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6192 (ttt-90) cc_final: 0.5661 (ptm160) REVERT: A 125 TRP cc_start: 0.6949 (t60) cc_final: 0.6736 (t60) REVERT: A 365 LYS cc_start: 0.7773 (tttp) cc_final: 0.7470 (mtpp) REVERT: A 421 GLN cc_start: 0.7211 (mm-40) cc_final: 0.6851 (mm110) REVERT: A 442 ARG cc_start: 0.7121 (ttp-170) cc_final: 0.6888 (tpp80) outliers start: 16 outliers final: 12 residues processed: 139 average time/residue: 0.2650 time to fit residues: 50.1588 Evaluate side-chains 138 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 103 optimal weight: 0.0470 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 61 optimal weight: 0.0270 chunk 108 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 0.0020 overall best weight: 0.3746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10489 Z= 0.119 Angle : 0.486 6.771 14191 Z= 0.250 Chirality : 0.041 0.163 1606 Planarity : 0.004 0.049 1769 Dihedral : 11.802 150.509 1790 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.83 % Allowed : 14.23 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.24), residues: 1259 helix: 1.69 (0.23), residues: 538 sheet: -0.15 (0.40), residues: 160 loop : -0.67 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1001 HIS 0.002 0.001 HIS A 569 PHE 0.012 0.001 PHE A 318 TYR 0.014 0.001 TYR A 881 ARG 0.003 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6113 (ttt-90) cc_final: 0.5601 (ptm160) REVERT: A 125 TRP cc_start: 0.6915 (t60) cc_final: 0.6703 (t60) REVERT: A 365 LYS cc_start: 0.7781 (tttp) cc_final: 0.7465 (mtpp) REVERT: A 421 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6707 (mm-40) REVERT: A 457 ARG cc_start: 0.6889 (mtt180) cc_final: 0.6505 (mtt-85) REVERT: A 473 GLU cc_start: 0.7468 (tp30) cc_final: 0.7037 (tp30) REVERT: A 988 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7958 (p) REVERT: B 229 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6646 (mm-30) outliers start: 9 outliers final: 7 residues processed: 135 average time/residue: 0.2704 time to fit residues: 49.4734 Evaluate side-chains 132 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS A 569 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10489 Z= 0.160 Angle : 0.498 7.427 14191 Z= 0.254 Chirality : 0.042 0.288 1606 Planarity : 0.004 0.049 1769 Dihedral : 11.727 152.620 1790 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.47 % Allowed : 14.60 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.24), residues: 1259 helix: 1.69 (0.23), residues: 538 sheet: -0.23 (0.39), residues: 161 loop : -0.64 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1001 HIS 0.002 0.001 HIS A 569 PHE 0.013 0.001 PHE A 935 TYR 0.019 0.001 TYR A 805 ARG 0.003 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6190 (ttt-90) cc_final: 0.5646 (ptm160) REVERT: A 125 TRP cc_start: 0.6961 (t60) cc_final: 0.6750 (t60) REVERT: A 365 LYS cc_start: 0.7787 (tttp) cc_final: 0.7475 (mtpp) REVERT: A 421 GLN cc_start: 0.7099 (mm-40) cc_final: 0.6724 (mm-40) REVERT: B 220 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7395 (pm20) REVERT: B 229 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6616 (mm-30) outliers start: 16 outliers final: 11 residues processed: 143 average time/residue: 0.2742 time to fit residues: 53.1198 Evaluate side-chains 141 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 48 optimal weight: 30.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10489 Z= 0.157 Angle : 0.504 7.289 14191 Z= 0.257 Chirality : 0.042 0.294 1606 Planarity : 0.004 0.049 1769 Dihedral : 11.554 153.272 1790 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.11 % Allowed : 14.23 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.24), residues: 1259 helix: 1.69 (0.23), residues: 537 sheet: -0.27 (0.39), residues: 164 loop : -0.60 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 430 HIS 0.002 0.000 HIS A 868 PHE 0.013 0.001 PHE A 935 TYR 0.016 0.001 TYR A 881 ARG 0.004 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6177 (ttt-90) cc_final: 0.5650 (ptm160) REVERT: A 125 TRP cc_start: 0.6952 (t60) cc_final: 0.6748 (t60) REVERT: A 365 LYS cc_start: 0.7780 (tttp) cc_final: 0.7454 (mtpp) REVERT: A 421 GLN cc_start: 0.7188 (mm-40) cc_final: 0.6703 (mm-40) REVERT: A 501 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7288 (pp30) REVERT: B 220 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7388 (pm20) REVERT: B 229 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6617 (mm-30) outliers start: 23 outliers final: 17 residues processed: 149 average time/residue: 0.2480 time to fit residues: 50.7702 Evaluate side-chains 147 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 109 optimal weight: 0.0070 chunk 115 optimal weight: 0.3980 chunk 105 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 10489 Z= 0.139 Angle : 0.563 16.099 14191 Z= 0.274 Chirality : 0.043 0.308 1606 Planarity : 0.004 0.049 1769 Dihedral : 11.467 153.188 1790 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.84 % Allowed : 15.06 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.24), residues: 1259 helix: 1.86 (0.23), residues: 531 sheet: -0.11 (0.39), residues: 161 loop : -0.59 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1001 HIS 0.001 0.000 HIS A 57 PHE 0.019 0.001 PHE B 264 TYR 0.018 0.001 TYR A 805 ARG 0.003 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6199 (ttt-90) cc_final: 0.5676 (ptm160) REVERT: A 125 TRP cc_start: 0.6960 (t60) cc_final: 0.6750 (t60) REVERT: A 365 LYS cc_start: 0.7749 (tttp) cc_final: 0.7427 (mtpp) REVERT: A 421 GLN cc_start: 0.7007 (mm-40) cc_final: 0.6660 (mm-40) REVERT: A 501 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7293 (pp30) REVERT: B 220 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7316 (pm20) REVERT: B 229 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6580 (mm-30) REVERT: B 266 ASN cc_start: 0.6888 (m-40) cc_final: 0.6670 (m-40) outliers start: 20 outliers final: 14 residues processed: 149 average time/residue: 0.2543 time to fit residues: 51.8723 Evaluate side-chains 147 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS A 860 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10489 Z= 0.201 Angle : 0.565 12.942 14191 Z= 0.282 Chirality : 0.044 0.308 1606 Planarity : 0.004 0.048 1769 Dihedral : 11.759 155.515 1790 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.02 % Allowed : 15.15 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.24), residues: 1259 helix: 1.67 (0.23), residues: 531 sheet: 0.05 (0.40), residues: 150 loop : -0.64 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 430 HIS 0.002 0.001 HIS A 868 PHE 0.026 0.001 PHE A 128 TYR 0.017 0.001 TYR A 881 ARG 0.002 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6255 (ttt-90) cc_final: 0.5745 (ptm160) REVERT: A 365 LYS cc_start: 0.7727 (tttp) cc_final: 0.7414 (mtpp) REVERT: A 421 GLN cc_start: 0.7227 (mm-40) cc_final: 0.6756 (mm-40) REVERT: A 501 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7295 (pp30) REVERT: B 220 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7327 (pm20) REVERT: B 229 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6600 (mm-30) REVERT: B 266 ASN cc_start: 0.6863 (m-40) cc_final: 0.6518 (m-40) outliers start: 22 outliers final: 17 residues processed: 152 average time/residue: 0.2592 time to fit residues: 53.5867 Evaluate side-chains 150 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 124 optimal weight: 0.2980 chunk 114 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 76 optimal weight: 0.0070 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 105 optimal weight: 0.0770 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10489 Z= 0.140 Angle : 0.531 10.840 14191 Z= 0.265 Chirality : 0.042 0.299 1606 Planarity : 0.004 0.049 1769 Dihedral : 11.467 154.623 1790 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.74 % Allowed : 15.52 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.24), residues: 1259 helix: 1.83 (0.23), residues: 531 sheet: -0.10 (0.39), residues: 161 loop : -0.57 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1001 HIS 0.002 0.000 HIS A 505 PHE 0.026 0.001 PHE A 128 TYR 0.014 0.001 TYR A 881 ARG 0.003 0.000 ARG A 442 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6249 (ttt-90) cc_final: 0.5723 (ptm160) REVERT: A 365 LYS cc_start: 0.7735 (tttp) cc_final: 0.7416 (mtpp) REVERT: A 421 GLN cc_start: 0.7029 (mm-40) cc_final: 0.6631 (mm-40) REVERT: A 457 ARG cc_start: 0.6911 (mtt180) cc_final: 0.6486 (mtt-85) REVERT: A 501 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7319 (pp30) REVERT: B 220 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7342 (pm20) REVERT: B 229 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6524 (mm-30) REVERT: B 266 ASN cc_start: 0.6759 (m-40) cc_final: 0.6370 (m-40) outliers start: 19 outliers final: 17 residues processed: 148 average time/residue: 0.2773 time to fit residues: 55.4615 Evaluate side-chains 148 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.154813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.119232 restraints weight = 12568.441| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.71 r_work: 0.2957 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10489 Z= 0.231 Angle : 0.581 10.836 14191 Z= 0.290 Chirality : 0.044 0.357 1606 Planarity : 0.004 0.047 1769 Dihedral : 11.959 157.122 1790 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.02 % Allowed : 15.61 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.24), residues: 1259 helix: 1.60 (0.23), residues: 531 sheet: 0.08 (0.40), residues: 149 loop : -0.62 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 430 HIS 0.002 0.001 HIS A 868 PHE 0.026 0.002 PHE A 128 TYR 0.018 0.001 TYR A 881 ARG 0.004 0.000 ARG A 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2281.64 seconds wall clock time: 41 minutes 25.52 seconds (2485.52 seconds total)